Configuration and geometry calculation

User 25d107bd42

06-01-2008 10:28:52

Using the internet-applet of MarvinSketch and doing the following:


1) Insert-Template-Amino Acids-L-Isolecin


2) Edit-Add-Absolute Stereo


Nothing happens, why ? (Using the on my machine installed


Marvin-programs I get the configuration assigned as 2S-3S, OK).





Then using in the applet


3) Tools-Geometry-Geometry


in the geometry window appears the 2R-3S configuration, why ?


In the steric hindrance window it is still 2S-3S.


(Same result in the applet and the installed program)


See screenshot149.png





Then using in the applet


4) Tools-Conformation-Conformers


all Conformers have the 2S-3S-configuration, OK.


See screenshot150.png





What is wrong in step 3) ?

ChemAxon 990acf0dec

06-01-2008 18:20:18

Thank you for the report. We will check what's wrong with the geometry plugin, and come back with the answer soon.

ChemAxon 8b644e6bf4

08-01-2008 16:17:36

Found a bug in the Geometry plugin. It will be corrected in the next release - thanks again for reporting it.

User 25d107bd42

08-01-2008 16:37:19

Thank you. The topic is very important for me.


I will give a course in February !





Above, I had a first question in my first post.


What's the answer for it ?

ChemAxon 8b644e6bf4

08-01-2008 17:20:39

In the View -> Misc -> R/S labels, select "ALL". (Having "up" - solid - or "down" - hatched - triangles specifies the stereo configuration for 3D generation. Displaying R/S labels can be turned off independently - which seems to be the default on the web demo.) For further info on "Add absolute stereo" see http://www.chemaxon.com/marvin/doc/user/stereo-doc.html.





You can work around the above mentioned bug (having wrong configuration in the Geometry plugin) in the current version the following way: before calling Tools -> Geometry -> Geometry, call Edit -> Clean -> 3D -> Clean in 3D. (If required, you can clean back to 2D in the steric hindrance window)

User 25d107bd42

08-01-2008 17:39:54

Thank you. I will try the workaround.





It would be fine, to have the default setting in the web demo


as "Displaying R/S labels in the main window",


as in the installed version.


It is a very good feature, you should show it to visitors of the web page.

ChemAxon 8b644e6bf4

14-01-2008 15:30:42

The web demo uses the default settings, while the installed applications uses the last used ones. This might explain the difference you experienced.